Congenital heart disease accounts for a large proportion of serious birth defects. The pathologic anatomy of these malformations may result from sequential alterations in normal embryonic development. In this study, embryo observations, autopsy observations, and theories of pathogenesis are all translated into symbolic logic, and each patient's disease is analyzed individually, as a functional unit. Specific malformation complexes to be investigated are: atrioventricular canal defects, persistent left superior vena cava, asplenia/polysplenia, transposition of the great vessels, double-outlet right ventricle, double-inlet left ventricle and corrected transposition. Since many patients with congenital heart disease have a complex of defects, our analysis attempts to trace the patient's problems back to one or a few initiating events in cardiac morphogenesis. Our analysis favors theories of pathogenesis which accurately predict which anatomic lesions will or will not be found in association with one another. Accurate expectations of associated malformations can lead both to the development of more relevant experimental models, and to a more rational medical and surgical management of affected patients.